coot/source

cootをソースから作ってみる

本家様にこれを流せば作れるよなスクリプトが提供されてます.
https://www2.mrc-lmb.cam.ac.uk/personal/pemsley/coot/web/build-install-coot-from-scratch.html
っが一筋縄ではいかない...

目下 version 0.9.x と version 1.1.x の２系列が存在している.

ここでは version 0.9.x を作ってみます. version 1.1.x はこちら
使用するスクリプトはこちら
https://raw.githubusercontent.com/pemsley/coot/refinement/build-it

Rockylinux9†

[root@rockylinux9 ~]# cat /etc/redhat-release
Rocky Linux release 9.6 (Blue Onyx)
 
[root@rockylinux9 ~]# dnf groupinstall "Development Tools"
[root@rockylinux9 ~]# dnf install epel-release
 
[root@rockylinux9 ~]# dnf repolist all |grep enabled
appstream                     Rocky Linux 9 - AppStream                 enabled
baseos                        Rocky Linux 9 - BaseOS                    enabled
epel                          Extra Packages for Enterprise Linux 9 - x enabled
epel-cisco-openh264           Extra Packages for Enterprise Linux 9 ope enabled
extras                        Rocky Linux 9 - Extras                    enabled
[root@rockylinux9 ~]#
 
 
[root@rockylinux9 ~]# dnf install --enablerepo=devel cmake freetype-devel libpng-devel gtk2-devel libXt-devel mesa-libGLU-devel ncurses-devel gfortran libjpeg-turbo-devel libXpm-devel
[root@rockylinux9 ~]# dnf install http://mirror.ghettoforge.org/distributions/gf/el/9/gf/x86_64/libgnomecanvas-2.30.3-26.gf.el9.x86_64.rpm
 
[root@rockylinux9 ~]# mkdir script ; cd script
 
[root@rockylinux9 script]# wget https://raw.githubusercontent.com/pemsley/coot/refinement/build-it
 
[root@rockylinux9 script]# vi build-it

build-itの編集内容

--- build-it.orig       2025-08-17 23:51:14.829766444 +0900
+++ build-it    2025-08-17 23:55:39.027863798 +0900
@@ -1052,7 +1052,7 @@
 
    if [ -e /bin/rpm ] ; then
       if rpm -a ; then
-         for i in fedora-release redhat-release redhat-release-workstation centos-release sl-release openSUSE-release ; do
+         for i in fedora-release redhat-release redhat-release-workstation centos-release sl-release openSUSE-release rocky-release ; do
            dist=`rpm -q --qf '%{name}' ${i}`
            echo  dist is $dist
            dist=`rpm -q --qf '%{name}' ${i}`
@@ -1091,7 +1091,7 @@
     esac
     ;;
 
-    fedora | centos | openSUSE )
+    fedora | centos | openSUSE | rocky )
       systype=${architecture}-${dist_name}-${dist_ver}
     ;;
 
@@ -1524,8 +1524,8 @@
 # This setting of the alias fails.  It works on the command line.
 # WGET="LD_LIBRARY_PATH=/usr/lib wget -N -P ${AUTOBUILD_SOURCES}"
 # WGETO="LD_LIBRARY_PATH=/usr/lib wget   -P ${AUTOBUILD_SOURCES}"
-WGET="wget -N -P ${AUTOBUILD_SOURCES}"
-WGETO="wget   -P ${AUTOBUILD_SOURCES}"
+WGET="wget -N -P ${AUTOBUILD_SOURCES} --no-check-certificate"
+WGETO="wget   -P ${AUTOBUILD_SOURCES} --no-check-certificate"
 
 # latest version (without .tar.gz extension)
 coot_version=$fallback_coot_version
@@ -1619,6 +1619,7 @@
       coot_version=coot-0.9.8.9
       coot_version=coot-0.9.8.91
       coot_version=coot-0.9.8.92
+      coot_version=coot-0.9.8.96
       echo NNX:: coot_version $coot_version
 
    else
@@ -3378,6 +3379,7 @@
 
       boost_home_url=https://dl.bintray.com/boostorg/release/1.72.0/source
       boost_home_url=https://boostorg.jfrog.io/artifactory/main/release/1.72.0/source
+      boost_home_url=https://archives.boost.io/release/1.72.0/source
       echo wgetting $boost_home_url/boost_$boost_version.tar.gz
       ${WGET} $boost_home_url/boost_$boost_version.tar.gz
 
@@ -4593,8 +4595,8 @@
 # as is the case when one dose "make install"
 # So I will convert that to say just "../py-compile"
 #
-sed -ibackup -e 's/am__py_compile.*destdir.*/am__py_compile)/' pyrogen/Makefile
-sed -ibackup -e 's/am__py_compile.*destdir.*/am__py_compile)/' python/Makefile
+sed -ibackup -e 's/am__py_compile.*destdir.*/am__py_compile) \\/' pyrogen/Makefile
+sed -ibackup -e 's/am__py_compile.*destdir.*/am__py_compile) \\/' python/Makefile
 
 # these are no longer used
 #         --with-mmdb-prefix=$install_top_dir

っと修正した上で

[root@rockylinux9 script]# bash ./build-it
 :
(ティータイム)
 :
[root@rockylinux9 script]# ls -l ~/autobuild/
total 0
drwxr-xr-x.  4 root root  62 Aug 17 23:56 building
drwxr-xr-x.  9 root root  94 Aug 18 00:35 coot-Linux-x86_64-rocky-9.6-gtk2-python
drwxr-xr-x. 10 root root 112 Aug 18 00:34 Linux-rockylinux9-gtk2-python
[root@rockylinux9 script]#

この「~/autobuild/」に作られた「coot-Linux-x86_64-rocky-9.6-gtk2-python」が完成品. これを「/apps」に配置するなどして使う
だが、フォルダーパーミッション、ファイルパーミッションが微妙なフォルダ・ファイルがあるので修正しておきます

[root@rockylinux9 script]# ~/autobuild/coot-Linux-x86_64-rocky-9.6-gtk2-python
 
[root@rockylinux9 coot-Linux-x86_64-rocky-9.6-gtk2-python]# find . -type d ! -perm 755    <-- フォルダで755以外のパーミッションフォルダを探す
[root@rockylinux9 coot-Linux-x86_64-rocky-9.6-gtk2-python]# find . -type f ! -perm 644    <-- ファイルで644以外のパーミッションファイルを探す
 
[root@rockylinux9 coot-Linux-x86_64-rocky-9.6-gtk2-python]# find ./share/coot/data/assign-side-chains -type d -exec chmod 755 {} \;
[root@rockylinux9 coot-Linux-x86_64-rocky-9.6-gtk2-python]# find ./share/coot/data/assign-side-chains -type f -exec chmod 644 {} \;
 
[root@rockylinux9 coot-Linux-x86_64-rocky-9.6-gtk2-python]# find ./share/coot/lib/data/monomers -type d -exec chmod 755 {} \;
[root@rockylinux9 coot-Linux-x86_64-rocky-9.6-gtk2-python]# find ./share/coot/lib/data/monomers -type f -exec chmod 644 {} \;
 
[root@rockylinux9 coot-Linux-x86_64-rocky-9.6-gtk2-python]# cd ..

そして本番環境へコピー

[root@rockylinux9 ~]# mkdir /apps
[root@rockylinux9 ~]# mv autobuild/coot-Linux-x86_64-rocky-9.5-gtk2-python/ /apps/
 
あるいは
[root@rockylinux9 ~]# cd autobuild/
[root@rockylinux9 autobuild]# ls -l
total 0
drwxr-xr-x.  4 root root  62 Aug 17 23:56 building
drwxr-xr-x.  9 root root  94 Aug 18 00:35 coot-Linux-x86_64-rocky-9.6-gtk2-python
drwxr-xr-x. 10 root root 112 Aug 18 00:34 Linux-rockylinux9-gtk2-python
 
[root@rockylinux9 autobuild]# ar cvf   ~/coot-0.9.8.96-Linux-x86_64-rocky-9.6-gtk2-python.tar.gz   ./coot-Linux-x86_64-rocky-9.6-gtk2-python

EnvironmentModules は「/apps/modulefiles/coot」で内容は下記にします

#%Module1.0
set coot /apps/coot-Linux-x86_64-rocky-9.5-gtk2-python/
set-alias coot $coot/bin/coot

備考として
途中「~/public_html/build-logs/Linux-rockylinux9/gtk2-python-gcc-11_and_g++-11/」に各コンポーネントのコンパイルサマリが列挙されます.
全部を一つ一つ見て各コンポーネントが正常にコンパイルされてたかを確認できます.

っで起動してみると

となります。 MobaXtermのXは正しく表示される. Xmingだと背景色が白のままで一見動いていないように見える..MobaXtermの方がいいかも

libvpx-develは入れてはダメ. libgdのコンパイルに必要かなと入れたら他のコンパイルに支障が発生
python3-numpyもダメみたい. rdkitの構築にエラーになるっぽい

↑

Rockylinux8†

[root@rockylinux8 ~]# cat /etc/redhat-release
Rocky Linux release 8.10 (Green Obsidian)
[root@rockylinux8 ~]# dnf groupinstall "Development Tools" -y
[root@rockylinux8 ~]# dnf install cmake gtk2-devel gcc-gfortran libXt-devel mesa-libGLU-devel libtiff-devel gd-devel -y
[root@rockylinux8 ~]# dnf install https://raw.githubusercontent.com/rpmsphere/x86_64/master/p/pangox-compat-0.0.2-2.x86_64.rpm https://raw.githubusercontent.com/rpmsphere/x86_64/master/p/pangox-compat-devel-0.0.2-2.x86_64.rpm

っで下準備は完了

[root@rockylinux8 ~]# mkdir script; cd script
[root@rockylinux8 script]# wget https://raw.githubusercontent.com/pemsley/coot/refinement/build-it
 
[root@rockylinux8 script]# vi build-it

「build-it」の修正箇所は rockylinux9 と同じです.
っで

[root@rockylinux8 script]# bash ./build-it
 :
(ティータイム)
 :
[root@rockylinux8 script]# ls -l ~/autobuild/
total 0
drwxr-xr-x.  4 root root  62 Feb  1 21:53 building
drwxr-xr-x.  9 root root  94 Feb  1 22:35 coot-Linux-x86_64-rocky-8.10-gtk2-python
drwxr-xr-x. 10 root root 112 Feb  1 22:30 Linux-rockylinux8-gtk2-python
[root@rockylinux8 script]#

完成した「coot-Linux-x86_64-rocky-8.10-gtk2-python」を「/apps」に移します

[root@rockylinux8 ~]# cd /apps/
[root@rockylinux8 apps]# mv ~/autobuild/coot-Linux-x86_64-rocky-8.10-gtk2-python .

EnvironmentModules はこんな感じで
「/apps/modulefiles/coot」

#%Module1.0
set coot /apps/coot-Linux-x86_64-rocky-8.10-gtk2-python
set-alias coot $coot/bin/coot

↑

ubuntu22.04†

root@ubuntu22:~# cat /etc/os-release
 :
VERSION="22.04.3 LTS (Jammy Jellyfish)"
 :
root@ubuntu22:~# apt-get update
root@ubuntu22:~# apt install build-essential git cmake m4 libtool swig flex bison gfortran autoconf automake libssl-dev \
libxext-dev libxmu-dev libxt-dev libtinfo-dev libncurses5-dev libglu1-mesa-dev libjpeg-dev mesa-common-dev libgtk2.0-dev libgnomecanvas2-dev
 
root@ubuntu22:~# mkdir script; cd script
root@ubuntu22:~/script# wget https://raw.githubusercontent.com/pemsley/coot/refinement/build-it
 
root@ubuntu22:~/script# vi build-it

修正箇所は rockylinux8/9 と同じ. rocky部分は不要ですが.

root@ubuntu22:~/script# bash ./build-it
 :
(ティータイム)
 :
root@ubuntu22:~/script# ls -l ~/autobuild/
total 12
drwxr-xr-x  4 root root 4096  2月  1 23:10 building
drwxr-xr-x  9 root root 4096  2月  1 23:56 coot-Linux-x86_64-ubuntu-22.04.3-gtk2-python
drwxr-xr-x 10 root root 4096  2月  1 23:52 Linux-ubuntu22-gtk2-python
root@ubuntu22:~/script#
 
root@ubuntu22:~/script# mv ~/autobuild/coot-Linux-x86_64-ubuntu-22.04.3-gtk2-python/ /apps
 
root@ubuntu22:~/script# vi /apps/modulefiles/coot
#%Module1.0
set coot /apps/coot-Linux-x86_64-ubuntu-22.04.3-gtk2-python
set-alias coot $coot/bin/coot
 
root@ubuntu22:~/script#

↑

ubuntu24.04†

root@ubuntu24:~# cat /etc/os-release
 :
VERSION="24.04.1 LTS (Noble Numbat)"
 :
root@ubuntu24:~# apt-get update
root@ubuntu24:~# apt install build-essential git cmake m4 libtool swig flex bison gfortran autoconf automake libssl-dev \
libxext-dev libxmu-dev libxt-dev libncurses-dev libglu1-mesa-dev libjpeg-dev mesa-common-dev libgtk2.0-dev libgnomecanvas2-dev
 
libtinfo-dev libncurses5-dev
 
root@ubuntu24:~# mkdir script; cd script
root@ubuntu24:~/script# wget https://raw.githubusercontent.com/pemsley/coot/refinement/build-it
 
root@ubuntu24:~/script# vi build-it

修正箇所は rockylinux8/9とほぼ同じですが、ubuntu22とubutun24とでパッケージ名称が変更されたのでその修正を加味してます

--- build-it.orig       2025-02-02 00:31:06.647470647 +0900
+++ build-it    2025-02-02 00:30:45.677465438 +0900
@@ -1183,8 +1183,7 @@
        libxmu-dev
        libxt-dev
        libc6-dev
-       libtinfo-dev
-       libncurses5-dev
+       libncurses-dev
        libssl-dev
        libglu1-mesa-dev
        libjpeg-dev
@@ -1524,8 +1523,8 @@
 # This setting of the alias fails.  It works on the command line.
 # WGET="LD_LIBRARY_PATH=/usr/lib wget -N -P ${AUTOBUILD_SOURCES}"
 # WGETO="LD_LIBRARY_PATH=/usr/lib wget   -P ${AUTOBUILD_SOURCES}"
-WGET="wget -N -P ${AUTOBUILD_SOURCES}"
-WGETO="wget   -P ${AUTOBUILD_SOURCES}"
+WGET="wget -N -P ${AUTOBUILD_SOURCES} --no-check-certificate"
+WGETO="wget   -P ${AUTOBUILD_SOURCES} --no-check-certificate"
 
 # latest version (without .tar.gz extension)
 coot_version=$fallback_coot_version
@@ -1619,6 +1618,7 @@
       coot_version=coot-0.9.8.9
       coot_version=coot-0.9.8.91
       coot_version=coot-0.9.8.92
+      coot_version=coot-0.9.8.95
       echo NNX:: coot_version $coot_version
 
    else
@@ -3378,6 +3378,7 @@
 
       boost_home_url=https://dl.bintray.com/boostorg/release/1.72.0/source
       boost_home_url=https://boostorg.jfrog.io/artifactory/main/release/1.72.0/source
+      boost_home_url=https://archives.boost.io/release/1.72.0/source
       echo wgetting $boost_home_url/boost_$boost_version.tar.gz
       ${WGET} $boost_home_url/boost_$boost_version.tar.gz
 
@@ -4593,8 +4594,8 @@
 # as is the case when one dose "make install"
 # So I will convert that to say just "../py-compile"
 #
-sed -ibackup -e 's/am__py_compile.*destdir.*/am__py_compile)/' pyrogen/Makefile
-sed -ibackup -e 's/am__py_compile.*destdir.*/am__py_compile)/' python/Makefile
+sed -ibackup -e 's/am__py_compile.*destdir.*/am__py_compile) \\/' pyrogen/Makefile
+sed -ibackup -e 's/am__py_compile.*destdir.*/am__py_compile) \\/' python/Makefile
 
 # these are no longer used
 #         --with-mmdb-prefix=$install_top_dir

そうして構築へ

root@ubuntu24:~/script# bash ./build-it
 :
(紅茶タイム)
 :
root@ubuntu24:~/script# ls -l ~/autobuild/
total 12
drwxr-xr-x  4 root root 4096 Feb  2 00:32 building
drwxr-xr-x  9 root root 4096 Feb  2 01:17 coot-Linux-x86_64-ubuntu-24.04.1-gtk2-python
drwxr-xr-x 10 root root 4096 Feb  2 01:13 Linux-ubuntu24-gtk2-python
root@ubuntu24:~/script#
 
root@ubuntu24:~/script# mv ~/autobuild/coot-Linux-x86_64-ubuntu-24.04.1-gtk2-python /apps
 
root@ubuntu24:~/script# vi /apps/modulefiles/coot
#%Module1.0
set coot /apps/coot-Linux-x86_64-ubuntu-24.04.1-gtk2-python
set-alias coot $coot/bin/coot
 
root@ubuntu24:~/script#